Remember that a Hovering Flyer doesn't get to Skyfire; and a Zooming Flyer has to declare at the start of the shooting phase whether it will use Skyfire this turn; in which case it can only Snapfire at ground targets (except Skimmers and Jetbikes; it still gets to fire normally at those even on Skyfire mode).

For Grey Knights, your main options for anti-flyer are:StormravensPsybolt autocannon dreads (still need 6s to hit, but 4 S8 shots twin-linked are still pretty good).Aegis line or Bastion with Quad gun (or Icarus lascannon, if you've got someone with good BS to man it).Psycannons for pure volume of fire.

Remember that in objective missions, objectives are normally supposed to be Mysterious, which gives a 1/6 chance of any given objective granting Skyfire to any scoring unit which holds the objective during the game. I've had tactical marines or CSMs with heavy weapon hold them, or Blood Angel assault marines do it, trailing back guys to hold it while I move the meltaguns forward into 12" range to hit a flyer.